Atomistry » Zinc » PDB 5n2z-5nea » 5ndb
Atomistry »
  Zinc »
    PDB 5n2z-5nea »
      5ndb »

Zinc in PDB 5ndb: Crystal Structure of Metallo-Beta-Lactamase Spm-1 Complexed with Cyclobutanone Inhibitor

Enzymatic activity of Crystal Structure of Metallo-Beta-Lactamase Spm-1 Complexed with Cyclobutanone Inhibitor

All present enzymatic activity of Crystal Structure of Metallo-Beta-Lactamase Spm-1 Complexed with Cyclobutanone Inhibitor:
3.5.2.6;

Protein crystallography data

The structure of Crystal Structure of Metallo-Beta-Lactamase Spm-1 Complexed with Cyclobutanone Inhibitor, PDB code: 5ndb was solved by P.Hinchliffe, J.Spencer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.63 / 2.38
Space group P 42 2 2
Cell size a, b, c (Å), α, β, γ (°) 130.758, 130.758, 102.759, 90.00, 90.00, 90.00
R / Rfree (%) 18 / 21.8

Other elements in 5ndb:

The structure of Crystal Structure of Metallo-Beta-Lactamase Spm-1 Complexed with Cyclobutanone Inhibitor also contains other interesting chemical elements:

Chlorine (Cl) 9 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Metallo-Beta-Lactamase Spm-1 Complexed with Cyclobutanone Inhibitor (pdb code 5ndb). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of Metallo-Beta-Lactamase Spm-1 Complexed with Cyclobutanone Inhibitor, PDB code: 5ndb:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 5ndb

Go back to Zinc Binding Sites List in 5ndb
Zinc binding site 1 out of 6 in the Crystal Structure of Metallo-Beta-Lactamase Spm-1 Complexed with Cyclobutanone Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Metallo-Beta-Lactamase Spm-1 Complexed with Cyclobutanone Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:49.0
occ:1.00
 O A:HOH532 2.0 41.9 1.0
NE2 A:HIS262 2.1 44.7 1.0
OD2 A:ASP110 2.4 41.1 1.0
SG A:CYS220 2.5 41.7 1.0
O01 A:8TW412 2.5 59.2 0.9
CE1 A:HIS262 3.0 40.2 1.0
CD2 A:HIS262 3.1 39.4 1.0
CG A:ASP110 3.3 36.6 1.0
CB A:CYS220 3.4 33.5 1.0
OD1 A:ASP110 3.5 39.6 1.0
C07 A:8TW412 3.5 79.0 0.9
ZN A:ZN402 3.5 37.1 1.0
C02 A:8TW412 3.5 66.4 0.9
O10 A:8TW412 3.5 72.0 0.9
C08 A:8TW412 3.8 83.6 0.9
C03 A:8TW412 3.9 73.3 0.9
O09 A:8TW412 4.0 80.6 0.9
ND1 A:HIS262 4.1 45.3 1.0
CG A:HIS262 4.2 41.9 1.0
NE2 A:HIS106 4.3 35.4 1.0
NE2 A:HIS195 4.3 38.4 1.0
CE1 A:HIS106 4.4 35.4 1.0
CE1 A:HIS195 4.6 36.1 1.0
O14 A:8TW412 4.6 58.3 0.9
CB A:ASP110 4.7 29.6 1.0
CA A:CYS220 4.7 37.4 1.0
O A:HOH585 4.9 40.1 1.0

Zinc binding site 2 out of 6 in 5ndb

Go back to Zinc Binding Sites List in 5ndb
Zinc binding site 2 out of 6 in the Crystal Structure of Metallo-Beta-Lactamase Spm-1 Complexed with Cyclobutanone Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Metallo-Beta-Lactamase Spm-1 Complexed with Cyclobutanone Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:37.1
occ:1.00
 O A:HOH532 1.8 41.9 1.0
ND1 A:HIS108 2.0 31.0 1.0
NE2 A:HIS195 2.2 38.4 1.0
NE2 A:HIS106 2.2 35.4 1.0
CE1 A:HIS108 2.9 34.2 1.0
CD2 A:HIS106 2.9 27.7 1.0
CG A:HIS108 3.0 35.7 1.0
CD2 A:HIS195 3.1 34.5 1.0
CE1 A:HIS195 3.2 36.1 1.0
CE1 A:HIS106 3.3 35.4 1.0
CB A:HIS108 3.4 31.7 1.0
O09 A:8TW412 3.5 80.6 0.9
ZN A:ZN401 3.5 49.0 1.0
NE2 A:HIS108 4.0 35.6 1.0
OD1 A:ASP110 4.0 39.6 1.0
O10 A:8TW412 4.1 72.0 0.9
CD2 A:HIS108 4.1 36.4 1.0
O01 A:8TW412 4.1 59.2 0.9
CG A:HIS106 4.2 34.1 1.0
CG A:HIS195 4.2 40.9 1.0
CB A:CYS220 4.3 33.5 1.0
ND1 A:HIS195 4.3 38.4 1.0
C08 A:8TW412 4.3 83.6 0.9
SG A:CYS220 4.3 41.7 1.0
ND1 A:HIS106 4.3 36.9 1.0
OD2 A:ASP110 4.6 41.1 1.0
CG A:ASP110 4.7 36.6 1.0
C02 A:8TW412 4.9 66.4 0.9
CA A:HIS108 4.9 34.3 1.0

Zinc binding site 3 out of 6 in 5ndb

Go back to Zinc Binding Sites List in 5ndb
Zinc binding site 3 out of 6 in the Crystal Structure of Metallo-Beta-Lactamase Spm-1 Complexed with Cyclobutanone Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Metallo-Beta-Lactamase Spm-1 Complexed with Cyclobutanone Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn407

b:32.2
occ:0.63
 OD2 A:ASP35 1.9 38.4 1.0
NE2 A:HIS33 2.3 52.9 1.0
CG A:ASP35 2.6 50.3 1.0
OD1 A:ASP35 2.7 55.6 1.0
CD2 A:HIS33 3.3 52.4 1.0
CE1 A:HIS33 3.3 53.0 1.0
CB A:ASP35 4.1 46.9 1.0
ND1 A:HIS33 4.4 62.0 1.0
CG A:HIS33 4.4 57.1 1.0
CA A:ASP35 4.9 47.2 1.0

Zinc binding site 4 out of 6 in 5ndb

Go back to Zinc Binding Sites List in 5ndb
Zinc binding site 4 out of 6 in the Crystal Structure of Metallo-Beta-Lactamase Spm-1 Complexed with Cyclobutanone Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Metallo-Beta-Lactamase Spm-1 Complexed with Cyclobutanone Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:47.5
occ:1.00
 O B:HOH506 2.1 38.3 1.0
NE2 B:HIS262 2.2 38.1 1.0
OD2 B:ASP110 2.4 38.2 1.0
SG B:CYS220 2.4 39.5 1.0
O14 B:8TW409 2.5 62.4 0.8
CD2 B:HIS262 3.1 39.4 1.0
CE1 B:HIS262 3.2 34.1 1.0
CG B:ASP110 3.3 32.4 1.0
ZN B:ZN402 3.4 38.3 1.0
CB B:CYS220 3.4 36.4 1.0
OD1 B:ASP110 3.5 31.1 1.0
C02 B:8TW409 3.6 66.7 0.8
O10 B:8TW409 3.6 79.0 0.8
C07 B:8TW409 3.8 76.2 0.8
C08 B:8TW409 3.9 80.5 0.8
O09 B:8TW409 4.0 82.8 0.8
C03 B:8TW409 4.0 72.5 0.8
NE2 B:HIS195 4.2 34.3 1.0
NE2 B:HIS106 4.2 34.3 1.0
CG B:HIS262 4.3 39.0 1.0
ND1 B:HIS262 4.3 35.8 1.0
CE1 B:HIS106 4.4 35.4 1.0
CE1 B:HIS195 4.6 34.7 1.0
O01 B:8TW409 4.7 60.4 0.8
CB B:ASP110 4.7 26.3 1.0
CA B:CYS220 4.7 31.3 1.0
CD2 B:HIS195 4.9 36.9 1.0

Zinc binding site 5 out of 6 in 5ndb

Go back to Zinc Binding Sites List in 5ndb
Zinc binding site 5 out of 6 in the Crystal Structure of Metallo-Beta-Lactamase Spm-1 Complexed with Cyclobutanone Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Metallo-Beta-Lactamase Spm-1 Complexed with Cyclobutanone Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn402

b:38.3
occ:1.00
 O B:HOH506 2.1 38.3 1.0
NE2 B:HIS195 2.1 34.3 1.0
ND1 B:HIS108 2.2 34.1 1.0
NE2 B:HIS106 2.2 34.3 1.0
CD2 B:HIS106 3.0 33.8 1.0
CD2 B:HIS195 3.0 36.9 1.0
CE1 B:HIS108 3.1 40.0 1.0
CG B:HIS108 3.1 37.9 1.0
CE1 B:HIS195 3.2 34.7 1.0
CE1 B:HIS106 3.3 35.4 1.0
ZN B:ZN401 3.4 47.5 1.0
CB B:HIS108 3.4 35.0 1.0
O09 B:8TW409 3.6 82.8 0.8
OD1 B:ASP110 4.0 31.1 1.0
O14 B:8TW409 4.0 62.4 0.8
SG B:CYS220 4.2 39.5 1.0
CG B:HIS195 4.2 37.0 1.0
CG B:HIS106 4.2 37.0 1.0
ND1 B:HIS195 4.2 36.9 1.0
NE2 B:HIS108 4.2 35.6 1.0
CB B:CYS220 4.3 36.4 1.0
CD2 B:HIS108 4.3 33.9 1.0
O10 B:8TW409 4.3 79.0 0.8
ND1 B:HIS106 4.3 38.8 1.0
C08 B:8TW409 4.5 80.5 0.8
OD2 B:ASP110 4.5 38.2 1.0
CG B:ASP110 4.7 32.4 1.0
O B:HOH584 4.8 56.2 1.0
C02 B:8TW409 4.9 66.7 0.8
CA B:HIS108 4.9 33.2 1.0

Zinc binding site 6 out of 6 in 5ndb

Go back to Zinc Binding Sites List in 5ndb
Zinc binding site 6 out of 6 in the Crystal Structure of Metallo-Beta-Lactamase Spm-1 Complexed with Cyclobutanone Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Metallo-Beta-Lactamase Spm-1 Complexed with Cyclobutanone Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn406

b:42.6
occ:1.00
 OD1 B:ASP35 1.9 39.0 1.0
NE2 B:HIS33 2.1 39.0 1.0
CG B:ASP35 2.7 41.7 1.0
OD2 B:ASP35 2.8 48.3 1.0
CD2 B:HIS33 3.0 38.9 1.0
CE1 B:HIS33 3.1 41.8 1.0
CG2 B:THR41 4.0 38.0 1.0
CG B:HIS33 4.2 48.0 1.0
ND1 B:HIS33 4.2 43.3 1.0
CB B:ASP35 4.2 30.9 1.0
CA B:ASP35 4.7 39.1 1.0
O B:HOH540 4.9 43.0 1.0
N B:ASP35 5.0 41.2 1.0

Reference:

M.I.Abboud, M.Kosmopoulou, A.P.Krismanich, J.W.Johnson, P.Hinchliffe, J.Brem, T.D.W.Claridge, J.Spencer, C.J.Schofield, G.I.Dmitrienko. Cyclobutanone Mimics of Intermediates in Metallo-Beta-Lactamase Catalysis. Chemistry V. 24 5734 2018.
ISSN: ISSN 1521-3765
PubMed: 29250863
DOI: 10.1002/CHEM.201705886
Page generated: Sun Oct 27 22:45:30 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy